Biosystems最新文献_第7页

Senescence, change, and competition: When the desire to pick one model harms our understanding 衰老、变化和竞争：当选择一种模式的欲望损害了我们的理解力时。

IF 2 4区生物学

Biosystems Pub Date : 2024-11-12 DOI: 10.1016/j.biosystems.2024.105364

André C.R. Martins

{"title":"Senescence, change, and competition: When the desire to pick one model harms our understanding","authors":"André C.R. Martins","doi":"10.1016/j.biosystems.2024.105364","DOIUrl":"10.1016/j.biosystems.2024.105364","url":null,"abstract":"<div><div>The question of why we age is a fundamental one. It is about who we are, and it also might have critical practical aspects as we try to find ways to age slower. Or to not age at all. Different reasons point at distinct strategies for the research of anti-aging drugs. While the main reason why biological systems work as they do is evolution, for quite a while, it was believed that aging required another explanation. Aging seems to harm individuals so much that even if it has group benefits, those benefits were unlikely to be enough. That has led many scientists to propose non-evolutionary explanations as to why we age. But those theories seem to fail at explaining all the data on how species age. Here, I will show that the insistence of finding the one idea that explains it all might be at the root of the difficulty of getting a full picture. By exploring an evolutionary model of aging where locality and temporal changes are fundamental aspects of the problem, I will show that environmental change causes the barrier for group advantages to become much weaker. That weakening might help small group advantages to add up to the point they could make an adaptive difference. To answer why we age, we might have to abandon asking which models are correct. The full answer might come from considering how much each hypothesis behind each existing model, evolutionary and non-evolutionary ones, contributes to the real world’s solution.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"247 ","pages":"Article 105364"},"PeriodicalIF":2.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142632119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Neurobehavioral State hypothesis 神经行为状态假说。

IF 2 4区生物学

Biosystems Pub Date : 2024-11-08 DOI: 10.1016/j.biosystems.2024.105361

Luis Fernando Ontiveros-Araiza

{"title":"The Neurobehavioral State hypothesis","authors":"Luis Fernando Ontiveros-Araiza","doi":"10.1016/j.biosystems.2024.105361","DOIUrl":"10.1016/j.biosystems.2024.105361","url":null,"abstract":"<div><div>Since the early attempts to understand the brain made by Greek philosophers more than 2000 years ago, one of the main questions in neuroscience has been how the brain perceives all the stimuli in the environment and uses this information to implement a response. Recent hypotheses of the neural code rely on the existence of an ideal observer, whether on specific areas of the cerebral cortex or distributed network composed of cortical and subcortical elements. The Neurobehavioral State hypothesis stipulates that neurons are in a quasi-stable state due to the dynamic interaction of their molecular components. This increases their computational capabilities and electrophysiological behavior further than a binary active/inactive state. Together, neuronal populations across the brain learn to identify and associate internal and external stimuli with actions and emotions. Furthermore, such associations can be stored through the regulation of neuronal components as new quasi-stable states. Using this framework, behavior arises as the result of the dynamic interaction between internal and external stimuli together with previously established quasi-stable states that delineate the behavioral response. Finally, the Neurobehavioral State hypothesis is firmly grounded on present evidence of the complex dynamics within the brain, from the molecular to the network level, and avoids the need for a central observer by proposing the brain configures itself through experience-driven associations.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"247 ","pages":"Article 105361"},"PeriodicalIF":2.0,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142632070","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploring the spatial effects influencing the EGFR/ERK pathway dynamics with machine learning surrogate models 利用机器学习代用模型探索影响表皮生长因子受体/表皮生长受体激酶通路动态的空间效应。

IF 2 4区生物学

Biosystems Pub Date : 2024-11-07 DOI: 10.1016/j.biosystems.2024.105360

Juan A. Garcia, Anass Bouchnita

{"title":"Exploring the spatial effects influencing the EGFR/ERK pathway dynamics with machine learning surrogate models","authors":"Juan A. Garcia, Anass Bouchnita","doi":"10.1016/j.biosystems.2024.105360","DOIUrl":"10.1016/j.biosystems.2024.105360","url":null,"abstract":"<div><div>The fate of cells is regulated by biochemical reactions taking place inside of them, known as intracellular pathways. Cells display a variety of characteristics related to their shape, structure and contained fluid, which influences the diffusion of proteins and their interactions. To gain insights into the spatial effects shaping intracellular regulation, we apply machine learning (ML) to explore a previously developed spatial model of the epidermal growth factor receptor (EGFR) signaling. The model describes the reactions between molecular species inside of cells following the transient activation of EGF receptors. To train our ML models, we conduct 10,000 numerical simulations in parallel where we calculate the cumulative activation of molecules and transcription factors under various conditions such as different diffusion speeds, inactivation rates, and cell structures. We take advantage of the low computational cost of ML algorithms to investigate the effects of cell and nucleus sizes, the diffusion speed of proteins, and the inactivation rate of the Ras molecules on the activation strength of transcription factors. Our results suggest that the predictions by both neural networks and random forests yielded minimal mean square error (MSEs), while linear generalized models displayed a significantly larger MSE. The exploration of the surrogate models has shown that smaller cell and nucleus radii as well, larger diffusion coefficients, and reduced inactivation rates increase the activation of transcription factors. These results are confirmed by numerical simulations. Our ML algorithms can be readily incorporated within multiscale models of tumor growth to embed the spatial effects regulating intracellular pathways, enabling the use of complex cell models within multiscale models while reducing the computational cost.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"247 ","pages":"Article 105360"},"PeriodicalIF":2.0,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142632109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Adjustment of link weights based on tolerance promotes cooperation in spatial prisoner's dilemma game 根据容忍度调整链接权重，促进空间囚徒困境博弈中的合作。

IF 2 4区生物学

Biosystems Pub Date : 2024-11-05 DOI: 10.1016/j.biosystems.2024.105362

Shounan Lu , Yang Wang

{"title":"Adjustment of link weights based on tolerance promotes cooperation in spatial prisoner's dilemma game","authors":"Shounan Lu , Yang Wang","doi":"10.1016/j.biosystems.2024.105362","DOIUrl":"10.1016/j.biosystems.2024.105362","url":null,"abstract":"<div><div>Understanding and explaining cooperative behavior in human society has become an open question. In this paper, we propose a dynamic adjustment of pair relationships in a spatial prisoner's dilemma game. Unlike previous studies that individuals dynamically adjust the intensity of interaction with their opponents at each step, this work consider tolerance, in which the intensity of interaction is adjusted when the time of successive defections by an individual exceeds a tolerance threshold <em>T</em>. We find that although the proposed mechanism can significantly improve cooperation compared to traditional versions, a higher tolerance for continuous defection behavior is not conducive to the evolution of cooperation. Furthermore, an environmental adaptor that dynamically adjusts the paired relationship with the opponent at all times is beneficial for the evolution of cooperation. And the higher the degree of adjustment in the paired relationship, the lower the probability of continuous exploitation by defector. We hope that our work can provide some insights into explaining the existence and maintenance of cooperation.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105362"},"PeriodicalIF":2.0,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142606475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Human-driven evolution of cultivated plants and the origin of early civilizations: The concept of Neolithic revolution in the works of Nikolai Vavilov 人类推动的栽培植物进化和早期文明的起源：尼古拉-瓦维洛夫作品中的新石器革命概念。

IF 2 4区生物学

Biosystems Pub Date : 2024-10-30 DOI: 10.1016/j.biosystems.2024.105359

Abir U. Igamberdiev

{"title":"Human-driven evolution of cultivated plants and the origin of early civilizations: The concept of Neolithic revolution in the works of Nikolai Vavilov","authors":"Abir U. Igamberdiev","doi":"10.1016/j.biosystems.2024.105359","DOIUrl":"10.1016/j.biosystems.2024.105359","url":null,"abstract":"<div><div>The concept of centers of origin of cultivated plants (crop biodiversity hotspots) developed by Nikolai Vavilov (1887–1943) is essential for understanding the origin and evolution of human civilization. Vavilov formulated the principles of the Neolithic agricultural revolution and substantiated the basic patterns for the emergence of agricultural civilizations. He established that the center of speciation of the plants that have a potential for cultivation determines the origin of primary civilization. Humans actively performed the selection of plants with valuable properties, which led to the formation of new cultivated species and varieties, while the starting point for such unconsciously human-directed evolution was the presence of potentially useful traits due to the increased genetic diversity in the center of origin. The spreading of agriculturally important cultivars from the center of their origin led to the propagation of beneficial farming technologies over large areas. The establishment of human civilization resulted from the dynamic quasi-symbiotic relationship between humans and domesticated plants and animals, which human-driven evolution became an essential factor for the transformation and dynamics of human societies. In the addendum, we present archive materials on the cooperation of Nikolai Vavilov with the historians and ethnologists from the editorial board of the journal “Novy Vostok” (“Nouvel Orient”). These materials include his letters to Professor Ilya Borozdin.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"247 ","pages":"Article 105359"},"PeriodicalIF":2.0,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142565068","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Complex dynamic behavioral transitions in auditory neurons induced by chaotic activity 听觉神经元在混沌活动诱导下的复杂动态行为转换

IF 2 4区生物学

Biosystems Pub Date : 2024-10-22 DOI: 10.1016/j.biosystems.2024.105358

Guodong Huang, Shu Zhou, Rui Zhu, Yunhai Wang, Yuan Chai

{"title":"Complex dynamic behavioral transitions in auditory neurons induced by chaotic activity","authors":"Guodong Huang, Shu Zhou, Rui Zhu, Yunhai Wang, Yuan Chai","doi":"10.1016/j.biosystems.2024.105358","DOIUrl":"10.1016/j.biosystems.2024.105358","url":null,"abstract":"<div><div>Chaotic sequences are widely used in secure communication due to their high randomness. Chaotic resonance (CR) refers to the resonant response of a system to weak signals induced by chaotic activity, but its practical application remains limited. This study designs a simplified FitzHugh-Nagumo (FHN) auditory neuron model by simulating the physiological activities of auditory neurons and considering the combined stimulation of chaotic activity and sound signals. It is found that the neuron dynamics depend on both external sound stimuli and chaotic current intensity. Chaotic currents induce spikes in the neuron output sequence through CR, and the spikes become more frequent with increasing current intensity, eventually leading to a chaotic state regardless of the initial state. However, the sensitivity of the initial value of this chaotic sequence shifts to the chaotic current excitation system. The injection of chaotic currents can reduce the system's average Hamiltonian energy under certain conditions. By measuring the complexity of the generated sequences, we find that the addition of chaotic currents can enhance the complexity of the original sequences, and the enhancement ability increases with the intensity. This provides a new approach to enhance the complexity of original chaotic sequences. Moreover, different chaotic currents can induce different chaotic sequences with varying abilities to enhance the complexity of the original sequences. We hope our work can contribute to secure communication.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105358"},"PeriodicalIF":2.0,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142512370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Is there a bias in the codon frequency corresponding to homo-repeats found in human proteins? 人类蛋白质中的同源重复密码子频率是否存在偏差？

IF 2 4区生物学

Biosystems Pub Date : 2024-10-21 DOI: 10.1016/j.biosystems.2024.105357

Nikita V. Dovidchenko , Mikhail Yu. Lobanov , Oxana V. Galzitskaya

{"title":"Is there a bias in the codon frequency corresponding to homo-repeats found in human proteins?","authors":"Nikita V. Dovidchenko , Mikhail Yu. Lobanov , Oxana V. Galzitskaya","doi":"10.1016/j.biosystems.2024.105357","DOIUrl":"10.1016/j.biosystems.2024.105357","url":null,"abstract":"<div><div>It is well known that there is a codon usage bias in genomes, that is, some codons are observed more often than others. Codons implicated in the homo-repeats regions in human proteins are no exception. In this work, we analyzed the codon usage bias for all amino acid residues in homo-repeats larger than 4 in 3753 human proteins from 20447 protein sequences from the canonically reviewed human proteome. We have discovered that almost all homo-repeats in the human proteome, most of which encode Ala, Glu, Gly, Leu, Pro, and Ser (∼80% of all homo-repeats), have a codon usage bias, i.e. are mainly encoded by one codon. Moreover, there is a strong shift in homo-repeats in favor of the content of GC rich codons. Homo-repeats with Ala, Glu, Gly, Leu, Pro, and Ser predominate in the PDB, which has both ordered and disordered status. Examining the distribution of splicing sites, we found that about 15% of homo-repeats either contain or are located within 10 nucleotides of the splicing site, and Glu and Leu predominate in these homo-repeats. Our data is important for future study of the functions of homo-repeats, protein-protein interactions, and evolutionary fitness.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105357"},"PeriodicalIF":2.0,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142512371","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Dynamics of two feed forward genetic motifs in the presence of molecular noise 存在分子噪音时两种前馈遗传模式的动力学。

IF 2 4区生物学

Biosystems Pub Date : 2024-10-20 DOI: 10.1016/j.biosystems.2024.105352

Cooper Doe, David Brown, Hanqing Li

引用次数: 0

Intrinsic structural disorder on proteins is involved in the interactome evolution 蛋白质的内在结构紊乱参与了相互作用组的进化。

IF 2 4区生物学

Biosystems Pub Date : 2024-10-20 DOI: 10.1016/j.biosystems.2024.105351

Diego M. Bustos

引用次数: 0

Reality and imagination intertwined: A sensorimotor paradox interpretation 现实与想象交织：感官运动悖论解读》。

IF 2 4区生物学

Biosystems Pub Date : 2024-10-19 DOI: 10.1016/j.biosystems.2024.105350

Clémence Ortega Douville

{"title":"Reality and imagination intertwined: A sensorimotor paradox interpretation","authors":"Clémence Ortega Douville","doi":"10.1016/j.biosystems.2024.105350","DOIUrl":"10.1016/j.biosystems.2024.105350","url":null,"abstract":"<div><div>As a hypothesis on the origins of mind and language, the evolutionary theory of the sensorimotor paradox suggests that capacities for imagination, self-representation and abstraction would operate from a dissociation in what is known as the forward model. In some studies, sensory perception is understood as a system of prediction and confirmation (feedforward and feedback processes) that would share common yet distinct and overlapping neural networks with mental imagery. The latter would then mostly operate through internal feedback processes. The hypothesis of our theory is that dissociation and parallelism between those processes would make it less likely for imaginary prediction to match and simultaneously coincide with any sensory feedback, contradicting the stimulus/response pattern. The gap between the two and the effort required to maintain this gap, born from the development of bipedal stance and a radical change to our relation to our own hands, would be the very structural foundation to our capacity to elaborate abstract thoughts, by partially blocking and inhibiting motor action. Mental imagery would structurally be dissociated from perception, though maintaining an intricated relation of interdependence. Moreover, the content of the images would be subordinate to their function as emotional regulators, prioritising consistency with some global, conditional and socially learnt body-image. As a higher-level and proto-aesthetic function, we can speculate that the action and instrumentalisation of dissociating imagination from perception would become the actual prediction and their coordination, the expected feedback.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105350"},"PeriodicalIF":2.0,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479900","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0